Global proteomic analysis of sea urchin embryos reveals dynamic changes throughout embryogenesis

The sea urchin is a long-studied model used to study fertilization and various developmental processes. While its genome and transcriptomics data are well documented, the global quantitative proteomic dynamics that complement mRNA expression during development are not available. Here we utilize an "in-cell proteomics" strategy to profile the proteomic changes in 5 developmental time points (egg, 32-cell, blastula, gastrula and larva) of the purple sea urchin, Strongylocentrotus purpuratus. This strategy bypasses cell lysis needed in conventional proteomic experiments and detects over 6,000 protein groups using only 50 eggs/embryos. Over 3,000 proteins have significant changes throughout development that cluster into 6 unique expression patterns. Analysis of signaling proteins and some transcription factors involved in cell specification and differentiation align well with published literature, supporting that proteomes obtained reflect biology of the organism. Furthermore, a majority of mRNA and their corresponding protein levels are discordantly correlated across development. Overall, this study provides a comprehensive analysis of proteomic changes occurring throughout sea urchin development and establishes a powerful and sensitive high-throughput approach suitable for detecting proteomic changes with a small number of embryos.