Transcriptomic Analysis of Neocaridina denticulata sinensis Gills Following FPPS Knockdown Reveals Its Regulatory Role in Immune Response

Farnesyl pyrophosphate synthase (FPPS) is a key enzyme in the terpenoid biosynthesis pathway, responsible for converting isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) into farnesyl pyrophosphate (FPP). In crustaceans, FPPS plays an important role in various physiological processes, particularly in synthesizing the crustacean-specific hormone methyl farnesoate (MF). This study analyzed the evolutionary differences in the physicochemical properties, subcellular localization, gene structure, and motif composition of FPPS in <i>Neocaridina denticulata sinensis</i> (named NdFPPS) compared to other species. The significant evolutionary divergence of FPPS was observed in crustaceans, likely linked to its role in MF synthesis. After the RNA interference (RNAi)-mediated knockdown of <i>NdFPPS</i>, transcriptomic analysis of gills revealed the significant enrichment of differentially expressed genes (DEGs) in pathways related to metabolism and immunity. Gene set enrichment analysis (GSEA) showed that most of these immune-related pathways were significantly suppressed, suggesting that <i>NdFPPS</i> may indirectly regulate the immune response by modulating metabolic levels. During the early stages of <i>Vibrio parahaemolyticus</i> infection, the expression of <i>NdFPPS</i> in the gills was significantly downregulated and subsequently returned to its original levels. Overall, our results provide new perspectives on the role of FPPS in immune regulation and enrich the functional information of FPPS.