Transcriptomic and Proteomic Analyses of the Immune Mechanism in Pathogenetic and Resistant Chinese Soft-Shelled Turtle (Pelodiscus sinensis) Infected with Aeromonas hydrophila

Abstract

Background: As intensive aquaculture practices have progressed, the prevalence of bacterial diseases in the Chinese soft-shell turtle (Pelodiscus sinensis) has escalated, particularly infections caused by Aeromonas hydrophila, such as ulcerative dermatitis and abscess disease. Despite this, little is known about their immune defenses against this pathogen.

Methods: Our study pioneers an integrated analysis of transcriptomics and proteomics to investigate the immune responses of Chinese soft-shelled turtles to A. hydrophila infection.

Results: The investigation revealed significant differences in immune-related pathways between groups susceptible and resistant to A. hydrophila infection after 4 days. A total of 4667 and 3417 differentially expressed genes (DEGs), 763 and 568 differentially expressed proteins (DEPs), and 13 and 5 correlated differentially expressed genes and proteins (cor-DEGs-DEPs) were identified in susceptible and resistant Chinese soft-shelled turtles, respectively. In the resistant group, upregulation of immune-related genes, such as CD3ε and CD45, enhanced T-cell activation and the immune response. The proteomic analysis indicated that immune proteins, such as NF-κB1, were significantly upregulated in the resistant group. The correlation analysis between transcriptomics and proteomics demonstrated that the CD40 gene and protein, differentially expressed in the resistant group compared to the control group, were commonly upregulated within the Toll-like receptor signaling pathway.

Conclusions: The transcriptomic and proteomic data obtained from this study provide a scientific foundation for understanding the immune mechanisms that enable the Chinese soft-shelled turtle to resist A. hydrophila infection.

Keywords: Aeromonas hydrophila; Pelodiscus sinensis; immune mechanism; proteomic; transcriptomic.

Figure 1

HE-stained sections of spleen tissues from the control, resistant, and susceptible groups of Chinese soft-shelled turtles on the 4th day post-infection with A. hydrophila. (A) Control group (Group C); (B) resistant group (Group R); (C) susceptible group (Group S). Note: The scale bar represents 10 μm.

Figure 2

Volcano maps of significant DEGs. (A) TS-TC group; (B) TR-TC group. Note: Red dots represent upregulated DEGs; green dots represent downregulated DEGs.

Figure 3

GO classification statistics of DEGs. (A) TS-TC group; (B) TR-TC group. Note: Red bars represent the enrichment of upregulated DEGs at GO Level II. Green bars represent the enrichment of downregulated DEGs at GO Level II. The x-axis denotes the category names, and the y-axis denotes the number of genes and their corresponding percentage for each category.

Figure 4

KEGG enrichment analysis. (A) TS-TC group; (B) TR-TC group. Note: The size of the dots represents the number of DEGs; the color of the dots represents the p-value. The x-axis denotes the enrichment score.

Figure 5

GO function annotation results of DEPs. (A) PS-PC group; (B) PR-PC group. Note: Green bars represent biological processes; blue bars represent cellular components; red bars represent molecular functions.

Figure 6

KEGG analysis of significant DEPs. (A) PS-PC group; (B) PR-PC group. Note: The size of the dots represents the number of DEPs; the color of the dots represents the p-value; the x-axis denotes the enrichment score.

Figure 7

Co-expression network graph of DEPs related to immunity.

Figure 8

Quadrant plot of cor-DEGs-DEPs. (A) tpS-tpC group; (B) tpR-tpC group. Note: The gray dots represent no significant differences in gene and protein levels. The purple dots represent upregulation in both the gene and protein. The blue dots represent downregulation in both the gene and protein. The red dots represent downregulation of gene expression with upregulation of protein levels. The green dots represent upregulation of gene expression with downregulation of protein levels.

Figure 9

KEGG enrichment analysis of cor-DEGs-DEPs. (A) Enriched pathways of cor-DEGs-DEPs upregulated in tpS-tpC group; (B) enriched pathways of cor-DEGs-DEPs downregulated in tpS-tpC group; (C) Eeriched pathways of cor-DEGs-DEPs upregulated in tpR-tpC group. Note: The size of the dots represents the number of cor-DEGs-DEPs; the color of the dots represents the p-value; the x-axis denotes the enrichment score.

Figure 10

Comparison of relative fold changes between RNA-seq and qRT-PCR results among the TS-TC and TR-TC. Fold changes represented the ratio of gene expression, and β-actin was used as an internal reference. Data are expressed as mean ± SD.