Comparative proteomics and transcriptomics illustrate the allograft-induced stress response in the pearl oyster (Pinctada fucata martensii)

Implantation of a spherical nucleus into a recipient oyster is a critical step in artificial pearl production. However, the molecular mechanisms underlying the response of the pearl oyster to this operation are poorly understood. In this research, we used transcriptomic and proteomic analyses to examine allograft-induced changes in gene/ protein expression patterns in Pinctada fucata martensii 12 h after nucleus implantation. Transcriptome analysis identified 688 differential expression genes (DEGs) (FDR 0.01 and |fold change) 2). Using a 1.2-fold increase or decrease in protein expression as a benchmark for differentially expressed proteins (DEPs), 108 DEPs were reliably quantified, including 71 up-regulated proteins (DUPs) and 37 down-regulated proteins (DDPs). Further analysis revealed that the GO terms, including cellular process, biological regulation and metabolic process were considerably enriched. In addition, the transcriptomics analysis showed that Neuroactive ligand-receptor interaction, NF-kappa B signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway', Toll like receptor signaling pathway, and Notch signaling pathway were significantly enriched in DEGs. The proteomics analysis showed that ECM-receptor interaction, Human papillomavirus infection, and PI3K-Akt signaling pathway were significantly enriched in DEPs. The results indicate that these functions could play an important role in response to pear oyster stress at nucleus implantation. To assess the potential relevance of quantitative information between mRNA and proteins, using Ward's hierarchical clustering analysis clustered the protein/gene expression patterns across the experimental and control samples into six groups. To investigate the biological processes associated with the protein in each cluster, we identified the significantly enriched GO terms and KEGG pathways in the proteins in each cluster. Gene set enrichment analysis (GSEA) was used to reveal the potential protein or transcription pathways associated with the response to nuclear implantation. Thus, the study of P. f. martensii is essential to enhance our understanding of the molecular mechanisms involved in pearl biosynthesis and the biology of bivalve molluscs.

Automated summary

In this study, transcriptomic and proteomic analyses were used to investigate the gene/protein expression patterns in Pinctada fucata martensii 12 hours after nucleus implantation. The results revealed differential expression genes and proteins, as well as enriched signaling pathways, indicating their importance in the response to nucleus implantation. This research provides insights into the molecular mechanisms involved in pearl biosynthesis and the biology of bivalve molluscs.