Two-dimensional gel and shotgun proteomics approaches for the comparative evaluation of genetically modified maize

In the safety risk assessment of genetically modified (GM) crops, it is imperative to evaluate potential unintended effects derived from genetic manipulation. Here, we analyzed the differential proteomic signatures and compositional equivalence of two GM insect- and herbicide-resistant maize cultivars (named here as GM1 and GM2), extensively cultivated and commercialized in Brazil, and their respective conventional counterparts (CON1 and CON2). Complementary 2-DE-based and bottom-up shotgun proteomic analysis were used. All cultivars presented similar chemical compositions between the GMs and CONs, with values expected for Zea mays species. A total of 22 and 21 differentially expressed proteins (DEPs) were identified in the 2-DE proteomic analysis for the GM1 vs. CON1 and GM2 vs. CON2 comparisons, respectively. In same order, 11 and 16 DEPs were identified in the bottom-up shotgun proteomic. DEPs were related to various biological processes including metabolism, energy, storage, defense, and cell stress. Vicilin-like embryo storage protein, tubulin, ADP-glucose pyrophosphorylase endosperm large subunit, globulin-1, and cytosolic 3-phosphoglycerate kinase, were consistently identified using both proteomic approaches. Of particular interest, vicilin-like embryo, identified as a natural allergen in maize, was down-regulated in the GM1 event compared to CON1. Our findings provide insights into potential unintended effects revealed through proteomic methodologies, utilizing both gel-based and gel-free techniques to identify alterations in protein abundance influenced by transgenic modification.