School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, 98105, USA.
Taylor Shellfish Hatchery, Quilcene, Washington, USA.
BMC Genomics. 2020 Oct 19;21(1):723. doi: 10.1186/s12864-020-07127-3.
Protein expression patterns underlie physiological processes and phenotypic differences including those occurring during early development. The Pacific oyster (Crassostrea gigas) undergoes a major phenotypic change in early development from free-swimming larval form to sessile benthic dweller while proliferating in environments with broad temperature ranges. Despite the economic and ecological importance of the species, physiological processes occurring throughout metamorphosis and the impact of temperature on these processes have not yet been mapped out.
Towards this, we comprehensively characterized protein abundance patterns for 7978 proteins throughout metamorphosis in the Pacific oyster at different temperature regimes. We used a multi-statistical approach including principal component analysis, ANOVA-simultaneous component analysis, and hierarchical clustering coupled with functional enrichment analysis to characterize these data. We identified distinct sets of proteins with time-dependent abundances generally not affected by temperature. Over 12 days, adhesion and calcification related proteins acutely decreased, organogenesis and extracellular matrix related proteins gradually decreased, proteins related to signaling showed sinusoidal abundance patterns, and proteins related to metabolic and growth processes gradually increased. Contrastingly, different sets of proteins showed temperature-dependent abundance patterns with proteins related to immune response showing lower abundance and catabolic pro-growth processes showing higher abundance in animals reared at 29 °C relative to 23 °C.
Although time was a stronger driver than temperature of metamorphic proteome changes, temperature-induced proteome differences led to pro-growth physiology corresponding to larger oyster size at 29 °C, and to altered specific metamorphic processes and possible pathogen presence at 23 °C. These findings offer high resolution insight into why oysters may experience high mortality rates during this life transition in both field and culture settings. The proteome resource generated by this study provides data-driven guidance for future work on developmental changes in molluscs. Furthermore, the analytical approach taken here provides a foundation for effective shotgun proteomic analyses across a variety of taxa.
蛋白质表达模式是生理过程和表型差异的基础，包括在早期发育过程中发生的差异。太平洋牡蛎（Crassostrea gigas）在早期发育过程中经历了一个重大的表型变化，从自由游动的幼虫形式转变为固着的底栖生物，同时在温度范围广泛的环境中增殖。尽管该物种具有重要的经济和生态意义，但整个变态过程中的生理过程以及温度对这些过程的影响尚未被描绘出来。
为此，我们在不同温度条件下，全面描绘了太平洋牡蛎变态过程中 7978 种蛋白质的丰度模式。我们使用了一种多统计方法，包括主成分分析、方差分析-同时成分分析和层次聚类，同时结合功能富集分析来描述这些数据。我们确定了具有时间依赖性丰度的不同蛋白质组，这些蛋白质的丰度通常不受温度影响。在 12 天内，附着和钙化相关蛋白急剧减少，器官发生和细胞外基质相关蛋白逐渐减少，与信号转导相关的蛋白表现出正弦丰度模式，与代谢和生长过程相关的蛋白逐渐增加。相反，不同的蛋白质组表现出温度依赖性的丰度模式，与免疫反应相关的蛋白质在 29°C 下的丰度较低，与促进生长的分解代谢过程相关的蛋白质在 29°C 下的丰度较高。
虽然时间是变态蛋白质组变化的主要驱动因素，但温度诱导的蛋白质组差异导致了在 29°C 下促进生长的生理反应，与更大的牡蛎大小相对应，而在 23°C 下则导致了特定的变态过程和可能的病原体存在的改变。这些发现为为什么牡蛎在野外和养殖环境中经历这个生命过渡时可能会经历高死亡率提供了高分辨率的见解。本研究生成的蛋白质组资源为未来贝类发育变化的研究提供了数据驱动的指导。此外，我们采用的分析方法为各种分类群的有效 shotgun 蛋白质组学分析奠定了基础。
