Comprehensive transcriptomic and proteomic analyses identify intracellular targets for myriocin to induce Fusarium oxysporum f. sp. niveum cell death

Abstract

Background: Myriocin is a natural product with antifungal activity and is derived from Bacillus amyloliquefaciens LZN01. Our previous work demonstrated that myriocin can inhibit the growth of Fusarium oxysporum f. sp. niveum (Fon) by inducing membrane damage. In this study, the antifungal actions of myriocin against Fon were investigated with a focus on the effects of myriocin on intracellular molecules.

Results: Analysis of DNA binding and fluorescence spectra demonstrated that myriocin can interact with dsDNA from Fon cells. The intracellular-targeted mechanism of action was also supported by transcriptomic and proteomic analyses; a total of 2238 common differentially expressed genes (DEGs) were identified. The DEGs were further verified by RT-qPCR. Most of the DEGs were assigned metabolism and genetic information processing functions and were enriched in ribosome biogenesis in eukaryotes pathway. The expression of some genes and proteins in ribosome biogenesis in eukaryotes pathway was affected by myriocin, primarily the genes controlled by the C6 zinc cluster transcription factor family and the NFYA transcription factor. Myriocin influenced the posttranscriptional processing of gene products by triggering the main RI (retained intron) events of novel alternative splicing; myriocin targeted key genes (FOXG_09470) or proteins (RIOK2) in ribosome biogenesis in eukaryotes pathway, resulting in disordered translation.

Conclusions: In conclusion, myriocin was determined to exhibit activity against Fon by targeting intracellular molecules. The results of our study may help to elucidate the antifungal actions of myriocin against Fon.

Keywords: Expression of genes and proteins; Fusarium oxysporum f. sp. niveum; Intracellular molecules; Myriocin; Transcriptomic and proteomic.

Fig. 1

Analysis of the DNA-binding properties (a) and mode of action (b) of myriocin by gel retarding and fluorescence intensity assays, respectively. a Green right triangles show the electrophoretic mobility of Fon cell DNA bands. b The main diagram displays the changes in fluorescence intensity, and the small diagram shows the fluorescence inhibition rate of different concentrations of myriocin

Fig. 2

Functional annotation (a, b and c) and enrichment analysis (d and e) of common DEGs. The functional descriptions of the COG types are shown in Additional file 2: Table S3. GO categories and KEGG pathways significantly enriched (P < 0.05) are shown in the figure

Fig. 3

Heatmaps of the DEGs (a) and DEPs (b) and diagram of DEGs and corresponding DEG-encoded proteins in ribosome biogenesis in eukaryotes pathway. a Heatmap of DEGs. b Heatmap of DEPs. The colors indicate the expression level of the gene/protein [log10(TPM+1)]. The protein names are shown on the right, and KO names represent them. The correspondence of protein accession IDs and KO names are listed in Additional file 2: Table S4. c Each of the two linked frames represents a DEG and the DEG-encoded DEPs.

Fig. 4

Correlation analysis of expression levels among DEGs (a), PPI network of DEPs (b) and correlation analysis network of expression levels among DEPs-DEGs (c). a and b Each node represents a DEG/DEP, and connecting lines represent the correlation of DEGs/DEPs. The larger the node is, the more important it is in the network. c Fully connected network of DEPs and DEGs. The nodes with the cross represent proteins, and the nodes with the circle represent genes. The larger the DEP node is, the more relevant it is to DEGs in the network. In addition, the nodes in the circle present DEPs, and the encoding gene of the protein is not a significant DEG

Fig. 5

Venn diagram of AS type (a), functional enrichment of significant differentially expressed novel AS genes (b), Venn diagram (c) and number of DEPs (d). a Venn diagrams represent the common genes of significant novel AS events in CK1_VS_MIC and CK1_VS_8 MIC. b KEGG enrichment analysis of the common genes. c CK_VS_MIC S and CK_VS_8 MIC S represent the significant DEPs from the CK_VS_MIC and CK_VS_8 MIC treatments, respectively

Fig. 6

Expression level of controlled genes by TF (a) and TFs (b). a Controlled gene names by TF are shown on the right. b TF accession IDs were shown on the right. The TF accession IDs and controlled gene names by TF are listed in Additional file 2: Table S11

Fig. 7

Molecular docking model of myriocin-NFYA/RIOK2. a and b represent the models of myriocin-NFYA and myriocin-RIOK2, respectively. From left to right, ribbons, surfaces and detailed binding diagrams are shown. Left: rectangular boxes represent internal docking areas. Middle: detailed internal docking areas (the surface color of proteins is classified by aromaticity). Right: detailed the bonding of myriocin-NFYA/RIOK2. GLU90, ARG253, PRO119, LYS105, ASP246, GLY104, LEU190, PHE232, PRO195 and ILE235 are amino acid residues. Hydrogen bonds are shown in green dashed lines. Electrostatic are shown in orange dashed line. Hydrophobics are shown in pink dashed line

Fig. 8

Conceptual model illustrating the intracellular-targeted mechanism of myriocin action on Fon