Systematic Proteomics Study on the Embryonic Development of Danio rerio

The early development of zebrafish (Danio
rerio) is a complex and dynamic physiological process
involving cell division,
differentiation, and movement. Currently, the genome and transcriptome
techniques have been widely used to study the embryonic development
of zebrafish. However, the research of proteomics based on proteins
that directly execute functions is relatively vacant. In this work,
we apply label-free quantitative proteomics to explore protein profiling
during zebrafish’s embryogenesis, and a total of 5961 proteins
were identified at 10 stages of zebrafish’s early development.
The identified proteins were divided into 11 modules according to
weighted gene coexpression network analysis (WGCNA), and the characteristics
between modules were significantly different. For example, mitochondria-related
functions enriched the early development of zebrafish. Primordial
germ cell-related proteins were identified at the 4-cell stage, while
the eye development event is dominated at 5 days post fertilization
(dpf). By combining with published transcriptomics data, we discovered
some proteins that may be involved in activating zygotic genes. Meanwhile,
137 novel proteins were identified. This study comprehensively analyzed
the dynamic processes in the embryonic development of zebrafish from
the perspective of proteomics. It provided solid data support for
further understanding of the molecular mechanism of its development.

斑马鱼（Danio rerio）的早期发育是一项复杂且动态的生理过程，涵盖细胞分裂、分化与运动环节。目前，基因组学与转录组学技术已被广泛应用于斑马鱼胚胎发育研究。然而，以直接执行功能的蛋白质为研究对象的蛋白质组学相关研究仍相对匮乏。本研究采用无标记定量蛋白质组学技术，对斑马鱼胚胎发生过程中的蛋白质谱展开探究，最终在斑马鱼早期发育的10个阶段中共鉴定出5961种蛋白质。通过加权基因共表达网络分析（weighted gene coexpression network analysis, WGCNA），将鉴定得到的蛋白质划分为11个模块，且各模块间的特征存在显著差异。例如，线粒体相关功能在斑马鱼早期发育阶段显著富集。原始生殖细胞相关蛋白质在4细胞期即被鉴定到，而受精后5天（days post fertilization, dpf）则以眼部发育事件为主要特征。结合已发表的转录组学数据，本研究发现了若干可能参与合子基因激活的蛋白质。同时，本研究还鉴定出137种新型蛋白质。本研究从蛋白质组学视角全面解析了斑马鱼胚胎发育的动态过程，为进一步阐明其发育的分子机制提供了坚实的数据支撑。