Transcriptomic and proteomic insights into the immune response of the intestine to Aeromonas veronii infection in koi carp (Cyprinus carpio var. koi)

Abstract

Intestinal mucosal immunity serves as one of the primary barriers against pathogens. The immune mechanism involved in fish intestinal defense against bacterial infection still needs further investigation. To delve into the intestinal immune mechanisms of koi carp (Cyprinus carpio var. koi) against Aeromonas veronii infection, RNA-seq and isobaric tags for relative and absolute quantitation (iTRAQ)-coupled LC-MS/MS were employed. After A. veronii infection, 7224 differently expressed genes (DEGs) and 1482 differently expressed proteins (DEPs) were detected in the intestines of koi carp. Further, the integrated analysis of transcriptomic and proteomic data revealed that 471 DEGs were matched with the corresponding DEPs (named associated DEPs/DEGs). Among the 34 immune-related associated DEPs/DEGs, 21 were in the consistent expression tendency, whereas 13 were in the opposite tendency. Moreover, the immune-related associated DEPs/DEGs exhibiting consistent expression trends were predominantly enriched in nine pathways, with five of them being linked to innate immunity: ferroptosis, phagosome, complement and coagulation cascades, MAPK signaling pathway, and NLR signaling pathway. The expression patterns of tested genes detected using quantitative real-time PCR assay were consistent with the findings from RNA-Seq and iTRAQ. A potential offense and defense model between A. veronii and koi carp was established based on insights into the immune-related pathways, DEGs, and DEPs. Overall, our comprehensive transcriptome and proteome analysis allow us to better understand the intestinal mucosal immunity of teleost and the pathogenic mechanism of A. veronii.