Proteasomal and lysosomal protein signatures in surviving Meretrix meretrix after acute ammonia exposure

Ammonia stress can disturb cellular protein homeostasis, but the coordinated response of protein quality-control systems in the bivalve hepatopancreas is not well understood. Hard clams (Meretrix meretrix) were exposed for 96 h to nominal total ammonia nitrogen (TAN) concentrations of 0 (Ctrl), 1.17 (Low), or 11.7 mg L^-1 (High). The High concentration was based on an extrapolated 96 h median lethal concentration estimate: the estimate of 11.7 mg L^-1 was below the lowest non-control concentration tested (12.5 mg L^-1). The experimental unit was the tank (n = 3 per treatment), and hepatopancreata from five survivors in each tank were pooled. TAN was measured during exposure, but the numerical records were not retained; actual TAN and unionized-ammonia (NH₃) exposures are therefore unknown. diaPASEF-based data-independent acquisition proteomics identified 9437 proteins. Exploratory criteria identified 417, 613, and 625 differentially abundant proteins (DAPs) in Low versus Ctrl, High versus Ctrl, and High versus Low, respectively, whereas 2, 10, and 13 proteins remained significant after false-discovery-rate (FDR) correction. KEGG gene-set enrichment analysis showed positive proteasomal enrichment and negative lysosomal enrichment in both comparisons involving the High group. These comparisons share the same High samples and are not independent. Protein processing in the endoplasmic reticulum was also enriched in High versus Ctrl. GPX3 was lower in High than in Low (0.52-fold; FDR = 0.0104), but requires independent validation. The results describe protein-abundance patterns in 96 h survivors, not changes in pathway activity or degradation flux. The High-group profile may include both treatment responses and selection of more tolerant individuals.