Development of early embryonic stages before activation of the embryonic genome depends on sufficiently stored products of the maternal genome and adequate activation, deactivation, and relocation of proteins. To establish protein function, several posttranslational events (e.g. proteolytic activation, phosphorylation, or secretion) are frequently essential and thereby prevent prediction of protein abundance from transcript abundance. Consequently, proteomic studies are indispensable to characterise the molecular processes governing early embryonic development and to establish corresponding regulatory networks. Here, we present a quantitative proteome analysis of bovine zygotes and embryos at the 2-cell and 4-cell stage. Cumulus-oocyte complexes (COC) were prepared from bovine ovaries obtained from a local abattoir and selected for a compact layer of cumulus cells. In vitro maturation, fertilization, and embryo production were performed according to standard procedures. For quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, protein from batches of 50 MII oocytes (serving as a reference), zygotes, 2-cell and 4-cell stage embryos, respectively, was extracted. Quantitative proteome analysis of iTRAQ-labelled tryptic peptides was performed on an Orbitrap XL instrument (Thermo Fisher, Waltham, MA, USA) coupled to an Eksigent nano-liquid chromatography system (AB Sciex, Framingham, MA, USA). The tandem MS data were analysed by MASCOT and filtered for a false discovery rate (FDR) of <1%. Quantification of iTRAQ signals was accomplished with the Q+ module of the Scaffold software (Proteome Software Inc., Portland, OR, USA). t-Tests, ANOVA and principal component analysis (PCA) analysis were performed using R (R Core Development Team, Vienna, Austria). From 4 biological replicates, 1072 proteins were identified and quantified. Eighty-seven differed significantly in abundance between the 4 stages (log2 fold change ≥ |0.6|, P ≤ 0.05). The proteomes of 2-cell and 4-cell embryos differed most from the reference MII oocyte, and a considerable fraction of proteins continuously increases in abundance during the stages analysed. Bioinformatic analysis of abundance altered proteins provided evidence that the proteins RPS14 and HNRNPK involved in the p53 pathway play a major role during early development, as well as proteins of the lipid metabolism, in particular APOA1. Furthermore, a group of proteins (e.g. SPTBN1, PPP1CC, RABGAP1, STMN1, and WEE2) is engaged in mitosis. In addition, we detected relevant differences between transcript and protein abundance levels; for example, for WEE2. In conclusion, this study identified and quantified numerous proteins important for early embryogenesis so far not described in the mammalian system, and contributed protein profiles for key players previously described. Our results highlight the importance of innovative proteomic tools and workflows to complement transcriptome data of early embryogenesis.
Liquid Chromatography MALDI MS/MS for Membrane Proteome Analysis