*3.2. Ontology Analysis of the Identified Proteins*

We classified each protein into one of three ontology categories: biological processes, molecular function, and cell components. For the proteins significant when comparing treated wt vs. control wt, the biological processes that were found more enriched were: carbon fixation, response to zinc ion, detoxification, response to cadmium ion, response to abiotic stimulus, and response to stress (Figure 4A). Molecular function categories enriched for this comparison were: glutathione binding, oligopeptide binding, and glutathione transferase activity, while the cell compartments were: apoplast, plastoglobule, chloroplast stroma, thylakoid, photosynthetic membrane, cell wall, organelle envelope, cytosol, and plastid (Figure S5A). The biological processes showed a strong response to stress in general and to metals in particular, including cadmium, which is a component of CdS QDs. In the enriched molecular functions, we found a predominant role of glutathione, which suggests a general response to oxidative stress caused by CdS QDs exposure [24]. The cell compartment pinpoints the role of the chloroplast in the response to CdS QDs, as already found by Pagano et al. [16]. (Figure S5B). This is in keeping with the oxidative stress response prominent in molecular function, as found by Ruotolo et al. [15]. For the protein differences emerging in the comparison of treated *atnp*01 vs. control *atnp*01, the biological processes that were found most enriched were: protein refolding, response to cadmium ion, response to heat and temperature and response to stress (Figure 4B). For this pair, the enriched molecular function categories were: misfolded protein binding, protein folding chaperone and heat shock protein binding, while the cell components were: endoplasmic reticulum chaperon complex, secretory vesicle, apoplast, cell wall, and cytosol (Figure S5C). Here, it is possible to recognize in the biological process not only responses to abiotic stress and metals, but also a protein folding response which is again predominant in the molecular function. Therefore, it can be summarized that treatment of the mutant line *atnp*01 potentiated several proteolytic mechanisms. Thus, the cellular components affected by the treatment were the endoplasmic reticulum and cell wall where proteolysis is carried out by the cell (Figure S5D). For the proteins emerging in the comparison of treated *atnp*02 vs. control *atnp*02, the biological processes that were found more enriched were: protein refolding, response to cadmium ion, response to metal ion, response to catabolic process and response to abiotic stimulus (Figure 4C). Laware and colleagues [49] found that in seedlings of *Alium cepa* treated with TiO2 nanoparticles there was a strong dose-dependent proteolitic activity. For the molecular function of the same comparison the

enriched categories were: misfolded protein binding, protein folding chaperone, heat shock protein binding, and nucleoside-triphosphate activity (Figure S5E), while the cell components were: apoplast, plastid envelope, thylakoid, chloroplast envelope and stroma, vacuole, bounding membrane of organelles and cell-cell junction (Figure S5F). Treated *atnp*02 responded in the biological function category with a general stress response and one category of protein folding which is similar to the response of the *atnp*01. Similarly, in terms of molecular function the categories were predominantly related to protein readjustment. In this case, the chloroplast (Gapa1 and Gapa2) and the vacuole (Vps24-1) were involved in the treatment response, which indicates the presence of oxidative stress [16].

**Figure 4.** Gene ontology and analyses with n-fold enrichment = −log10 (Fisher's exact *p*-value) for Biological process in wt (**a**), *atnp*01 (**b**) and *atnp*02 (**c**).
