Peptide generation process in protoplasts. We used transcription profiling data to construct a model describing the peptidogenesis in protoplasts. Up-regulated genes associated with factors affecting the protein degradation, such as stress response leading to increase in ROS, immune reactions, and synthesis of stress hormones, are indicated. We inferred that some peptides are degraded to amino acids, while another fraction can be biologically active. The scheme also indicates up-regulated genes encoding proteases and peptide transporters, which also can contribute to the cell peptidome. Arrows show some genes that were up-regulated 2-fold. A complete list of genes and quantitative data for this experiment are given in Additional file 12.