## 3 Responses to Hg Exposure at Different Levels of Biological Organization in _Elodea nuttallii_
### Responses at the Proteome and Metabolome Level  
As mentioned above, transcriptomic targets gene expression level, but it is its protein that carries the function of a gene in the cell. Eventually, proteins have numerous cell functions involved in signaling and tolerance to abiotic stressors such as the metabolism of amino acids and sugars, the energy production, primary and secondary metabolites that have a key role for remodeling, and cell physiological repair in plants [44]. Proteomics inform not only on protein expression level but also on the occurrence of regulation at post-transcription level. However, the availability and completeness of a database with identified proteins profiles still limits its use [42]. Early proteomic study with 2D-DIGE in _E. nuttallii_ identified 30 proteins involved in energy (sugar metabolism, photosynthesis) and cell structure to be dysregulated by 24 h exposure to 4:10\({}^{-10}\) M Hfg [19] (Table 1). Those observations were in line with previous transcriptomic data, as similar functions were observed in regulated genes in _E. nuttallii_ exposed to IHg. On the other hand, 1:10\({}^{-10}\) M MMHg did not result in significant proteomic response, which is opposite to the transcriptomic observation of a higher number of genes regulated by MMHg than IHg exposure [25]. This discrepancy might come from a lower uptake (0.19 ug\(\cdot\)g\({}^{-1}\)) of MMHg in those conditions than for IHg (0.67 ug\(\cdot\)g\({}^{-1}\)). Nonetheless, a few years later, the effects of the same concentrations (4:10\({}^{-10}\) M IHg, 1:10\({}^{-10}\) M MMHg 24 h resulting in 0.98 and 0.81 ug\(\cdot\)g\({}^{-1}\) THg respectively) were analyzed by GC-MS- and LC-MS-targeting metabolites in a way that is complementary to other molecular approaches to confirm the Hg cellular toxicity pathway in _E. nuttallii_ (Table 1) [43]. In whole shoots, MMHg resulted in the significant regulation of 15 metabolites, while no metabolite was significantly regulated by IHg treatment. In the cytosol, IHg and MMHg exposure regulated three metabolites and four metabolites respectively [43]. Pathway analysis by the Kyoto Encyclopedia of Genes and Genomes (KEGG) of deregulated metabolites revealed that MMHg exposure resulted in biochemical changes in aminoacyl-tRNA biosynthesis, glycine, serine and threonine metabolism, nitrogen metabolism, arginine and proline metabolism, cyanoamino acid metabolism, while IHg treatment caused no significant variations at the pathway level. The data supported an impact of MMHg on N homeostasis, while IHg had a low impact. In sum, metabolomics highlighted that sub-lethal concentrations of IHg and MMHg resulted in significant changes in the nutrition pathways and induced a protective response. Moreover, significant differences in the responses supported different molecular toxicity pathways of MMHg and IHg. Indeed, MMHg affects components of the non-soluble compartment of cells, while IHg affects components of the soluble compartment of cells. This point might explain the absence of the effect of MMHg, measured by proteomics using 2D-DIGE, which is known to better identify soluble proteins. Another discrepancy was the observation of no effect on sugars measured by metabolomics, contrary to the previously reported significant regulation of genes and proteins involved in the metabolism of sugars. As such, we concluded that gene regulation happened to keep the level of those metabolites stable [20; 25; 37; 35]. Nonetheless this apparent disconnection can be explained in part by technical issues, as well as by the complexity of the metabolic network structure. Although the linear relationship of transcripts with protein levels and their biological functions is sometimes observed, in general there is a major discrepancy that results from the circular nature and branching of metabolic pathways, notably when regulatory loops are operating [45]. In addition, the transformation of a metabolite dependsmore on the kinetic specificities of enzymes than on the concentration of enzymes or metabolites.