Physiological and Multi-Omics Analysis in Leaves of Solanum americanum in Response to Cd Toxicity

Abstract

Phytoremediation is a green economic method to address soil cadmium (Cd) pollution, and Solanum americanum is considered a potential phytoremediation candidate. However, the underlying Cd response mechanisms of S. americanum remain unclear. In the current study, a hydroponic experiment with 160 μmol/L Cd stress was conducted, physiological and molecular indices were measured to explore the response of S. americanum leaves to Cd stress at different time points (0, 3, and 7 days). Our findings revealed that Cd stress inhibited plant growth. Moreover, Cd stress significantly increased Cd accumulation, as well as Chla content, Chla/b, activities of SOD and POD, and elevated MDA content in the leaves. Furthermore, transcriptomics, proteomics, and metabolomics analyses revealed 17,413 differentially expressed genes (DEGs), 1421 differentially expressed proteins (DEPs), and 229 differentially expressed metabolites (DEMs). Meanwhile, integrative analyses of multi-omics data revealed key proteins involved in response to Cd stress, including POD, PAL, F5H, COMT, and CAD for phenylpropanoid biosynthesis, as well as GAPA, FBP, and FBA for photosynthesis pathways. Additionally, conjoint analyses highlighted that upregulated phenylpropanoid metabolism and photosynthesis alleviated Cd toxicity, playing vital roles in enhancing Cd tolerance in leaves. A conceptual molecular regulatory network of leaves in the response to Cd toxicity was proposed. This comprehensive study will provide detailed molecular-scale insights into the Cd response mechanisms in S. americanum.

Keywords: Cd stress; Solanum americanum; leaf; metabolomics; proteomic; transcriptomic.

Figure 1

Physiological response in leaves of S. americanum under Cd stress. (a) Biomass of plant and leaf; (b) Cd concentration of plant and leaf; (c) content of Chla, Chlb, and Chla/b in leaf; (d) activity of SOD, POD, and MDA content in leaf; values are the mean ± SE (n = 3), different lowercase letters indicate significant differences at different time points in the same tissue (p < 0.05), and “*” indicates significant difference between Cd-treated and control plants.

Figure 2

Analysis of gene expression levels in the leaves of S. americanum under Cd stress. (a) The number of Cd-responsive DEGs in leaves at different Cd stress time points; (b) Venn diagram summarizing all identified DEGs; Venn diagram summarizing overlapping upregulated (c) and downregulated (d) DEGs in leaves at different Cd stress time points; (e,f) histograms showing GO enrichment of DEGs in leaves at different Cd stress time points; (g,h) bubble diagrams showing KEGG pathway annotation of DEGs in leaves at different Cd stress time points (showing the top 15 most significantly enriched pathways, p < 0.05).

Figure 3

Analysis of protein expression levels in the leaves of S. americanum under Cd stress. (a) The number of Cd-responsive DEPs in leaves at different Cd stress time points; (b) Venn diagram summarizing all the identified DEPs; Venn diagram summarizing overlapping upregulated (c) and downregulated (d) DEPs in leaves at different Cd stress time points; (e,f) KEGG enrichment analysis of upregulated DEPs in leaves at different Cd stress time points; (g,h) KEGG enrichment of downregulated DEPs in leaves at different Cd stress time points.

Figure 4

Analysis of metabolite abundance levels in leaves of S. americanum under Cd stress. (a) The number of Cd-responsive DEMs in leaves at different Cd stress time points; (b) Venn diagram summarizing all the identified DEMs; Venn diagram summarizing the overlapping upregulated (c) and downregulated (d) DEMs in leaves at different Cd stress time points; (e,f) bubble diagram showing KEGG pathway annotations of DEMs in leaves at different Cd stress time points.

Figure 5

Joint analysis of transcriptomic, proteomic, and metabolomic data in leaves of S. americanum under Cd stress. (a) Venn diagram of KEGG pathways in DEGs/DEPs/DEMs for 3 d; (b) Venn diagram of KEGG pathway in DEGs/DEPs/DEMs for 7 d; (c) Venn diagram of KEGG pathway for 3 d and 7 d; (d) Common KEGG pathways annotated by Cd-responsive DEGs/DEPs/DEMs in leaves. Pathway classification: Ⅰ. Amino acid metabolism; Ⅱ. Carbohydrate metabolism; Ⅲ. Energy metabolism; Ⅳ. Lipid metabolism; Ⅴ. Biosynthesis of other secondary metabolites; Ⅵ. Nucleotide metabolism; Ⅶ. Metabolism of cofactors and vitamins; Ⅷ. Metabolism of terpenoids and polyketides; Ⅸ. Translation, and Ⅹ. Signal transduction.

Figure 6

Association analysis of transcriptomic and proteomic data in leaves of S. americanum under Cd stress. (a) Cd-responsive DEGs/DEPs in leaves at different Cd stress time points; (b) the number of co-regulated Cd-responsive DEGs/DEPs; KEGG enrichment analysis of upregulated DEGs/DEPs in leaves under Cd stress for 3 d (c) and 7 d (d); KEGG enrichment analysis of downregulated DEGs/DEPs in leaves under Cd stress for 3 d (e) and 7 d (f). “BU” indicates DEP/DEG both upregulated, “BD” indicates DEP/DEG both downregulated, “PUTD” indicates DEP upregulated but DEG downregulated, “PDTU” indicates DEP downregulated but DEG upregulated.

Figure 7

Chord diagrams of DEPs enrichment in leaves of S. americanum under Cd stress.

Figure 8

DEGs, DEPs, and DEMs involved in the phenylpropanoid biosynthesis pathway in the leaves of S. americanum under Cd stress.

Figure 9

DEGs, DEPs, and DEMs involved in the photosynthesis pathway in the leaves of S. americanum under Cd stress.

Figure 10

Molecular regulatory network in leaves of S. americanum in response to Cd stress. The red dot conceptually represents Cd²⁺.