Inhibition Molecular Mechanism of the Novel Fungicidal N-(Naphthalen-1-yl) phenazine-1-carboxamide against Rhizoctonia solani

Abstract

To explore the molecular mechanism through which the novel fungicide N-(naphthalen-1-yl) phenazine-1-carboxamide (NNPCN) inhibits Rhizoctonia solani, we clarified the target and mode of action, explored lead compounds, and developed novel fungicides. Methods: Growth observation, scanning electron microscopy, transmission electron microscopy, transcriptome sequencing technology, quantitative real-time PCR (qRT-PCR), physiological and biochemical determination, and reverse molecular docking technology were used to study the effects of this compound on the microscopic morphology of R. solani. The differentially expressed genes (DEGs), functions, and metabolic pathways were analyzed. The genes displaying significant differences were randomly selected for qRT-PCR verification and confirmed by physiological and biochemical determination to construct their binding mode with key targets. The results showed that the mycelium treated with NNPCN produced a red secretion and exhibited progressive creeping growth. Under a scanning electron microscope, hyphal swelling, uneven thickness, fractures, deformities, and hyphal surface warts increased. Under a transmission electron microscope, the cell wall was separated, the subcellular organelles were disintegrated, and the septum disappeared. Furthermore, there were 6838 DEGs under NNPCN treatment, including 291 significant DEGs, of which 143 were upregulated and 148 downregulated. Ten DEGs were randomly selected for qRT-PCR verification, and the gene expression trend was consistent with the transcriptome sequencing results. Gene Ontology enrichment analysis showed that the DEGs were significantly enriched in cell wall glucan decomposition and metabolism, cell membrane synthesis, metabolism, composition, organic hydroxyl compounds, oxidoreductase activity, and transition metal ion binding. Metabolic pathway enrichment analysis showed that there were 16 significant metabolic pathways, such as steroid biosynthesis and ABC transporters. Further study found that genes, such as the glycosyl hydrolase family 10 domain-containing protein, which is related to glucan catabolic process function as tied to the cell wall, were downregulated. Lipid oxidation, modification, and other genes related to the cell membrane were also downregulated. Secondly, genes related to lipid modification, lipid metabolism processes, integral components of the membrane, and other ABC transporters were downregulated. Fatty-acid oxidation and carbohydrate metabolic processes, which are related to antioxidant and metabolic functions, displayed significant differences in their target genes. Nitrite reductase [NADH] activity and mitochondrial organization gene expression were downregulated. These results revealed that target genes may involved in the cell wall, cell membrane, antioxidant and metabolism, nitrogen metabolism, and mitochondria. The results of the physiological and biochemical tests showed that NNPCN decreased the β-1,3-glucanase, malondialdehyde, and ATPase activities and nucleic acid leakage but increased the activity of nitrate reductase. The results of the reverse molecular docking showed that NNPCN could freely bind to target proteins such as β-1,3-glucanase, ABC transporter, and NADPH nitrate reductase, whereby NNPCN could bind to glucanase via van der Waals and electrostatic forces and to ABC transporter and NADPH nitrate reductase via hydrogen bonding. Conclusion: The mechanism via which NNPCN inhibits R. solani may be related to the cell wall structure, cell membrane damage, antioxidant activity, and metabolism.