Quantitative proteomic analysis of Araucaria angustifolia (Bertol.) Kuntze cell lines with contrasting embryogenic potential

GeLC–MS/MS based label free proteomic profiling was used in the large scale identification and quantification of proteins from Brazilian pine (Araucaria angustifolia) embryogenic cell (EC) lines that showed different propensities to form somatic embryos. Using a predicted protein sequence database that was derived from A. angustifolia RNA-Seq data, 2398 non-redundant proteins were identified. The log2 of the spectral count values of 858 proteins of these proteins showed a normal distribution, and were used for statistical analysis. Statistical tests indicated that 106 proteins were significantly differentially abundant between the two EC lines, and that 35 were more abundant in the responsive genotype (EC line SE1) and 71 were more abundant in the blocked genotype (EC line SE6). An increase in the abundance of proteins related to cell defense, anti-oxidative stress responses, and storage reserve deposition was observed in SE1. Moreover, in SE6 we observed an increased abundance of two proteins associated with seed development during the embryogenic cell proliferation stage, which we suggest is associated with genotypes showing a low responsiveness to embryo formation. Differences in protein abundance between the EC lines are discussed in terms of carbohydrate metabolism, cell division, defense response, gene expression, and response to reactive oxygen species.