A method for reducing the level of one or more than one protein in a plant or a tissue within the plant, and plants with reduced levels of target proteins are provided. The method involves introducing a nucleic acid sequence into the plant, where the nucleic acid sequence comprises a regulatory region operatively associated with a silencing nucleotide sequence. The expression of the silencing nucleotide sequence reduces or eliminates the expression of two or more than two enzymes involved in the synthesis of the one or more than one protein. The reduced level of the one or more than one protein may be determine by comparing the level of the one or more than one protein in the plant, or a tissue of the plant, with a level of the one ore more than one protein in a second plant, or the tissue from the second plant, that does not express the nucleic acid sequence. Plants and seeds obtained from plants with reduced levels of target proteins, and reduced anti-nutrient factors are also provided