Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
Fisheries College of Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, Guangdong, 524088, China.
Fish Shellfish Immunol. 2022 Feb;121:74-85. doi: 10.1016/j.fsi.2021.12.055. Epub 2022 Jan 3.
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.
将球形珠核植入贝类是人工育珠的关键步骤。然而，珍珠贝对此操作的反应的分子机制尚不清楚。在这项研究中，我们使用转录组和蛋白质组分析来研究珍珠贝在植入珠核 12 小时后的同种异体移植诱导基因/蛋白质表达模式的变化。转录组分析鉴定了 688 个差异表达基因（DEGs）（FDR<0.01 和 |fold change|>2）。使用蛋白质表达增加或减少 1.2 倍作为差异表达蛋白（DEPs）的基准，可靠地定量了 108 个 DEPs，包括 71 个上调蛋白（DUPs）和 37 个下调蛋白（DDPs）。进一步分析表明，GO 术语，包括“细胞过程”、“生物调节”和“代谢过程”显著富集。此外，转录组分析表明，DEGs 中显著富集了“神经活性配体-受体相互作用”、“NF-kappa B 信号通路”、“MAPK 信号通路”、“PI3K-Akt 信号通路”、“Toll 样受体信号通路”和“Notch 信号通路”。蛋白质组分析表明，DEPs 中“ECM-受体相互作用”、“人乳头瘤病毒感染”和“PI3K-Akt 信号通路”显著富集。结果表明，这些功能可能在珍珠贝对珠核植入的应激反应中发挥重要作用。为了评估 mRNA 和蛋白质之间定量信息的潜在相关性，使用 Ward 层次聚类分析将实验和对照样本中的蛋白质/基因表达模式聚类为六个组。为了研究与每个聚类中的蛋白质相关的生物学过程，我们确定了每个聚类中蛋白质显著富集的 GO 术语和 KEGG 途径。基因集富集分析（GSEA）用于揭示与核植入反应相关的潜在蛋白质或转录途径。因此，对 P. f. martensii 的研究对于增强我们对珍珠生物合成和双壳类软体动物生物学中涉及的分子机制的理解至关重要。
