**3. Proteomics**

Proteomics can be defined as the large-scale study of proteins, including not only their iden‐ tifications and quantifications, but also the determination of their localizations, modifica‐ tions, interactions, activities, and functions [55]. This information is extremely important to evaluate interactions between different proteins, or between proteins and other molecules, and may reveal the functional role of proteins [56]. In this sense, proteomics is an important part of plant science, providing essential tools for understanding the functions of many plant-specific biological processes at the molecular level [57]. Currently, plant proteomic studies are focused on understanding the impact of different conditions of plant physiology such as the characterization of plant defense under biotic and abiotic stress [58,59], the char‐ acterization of subcellular, cellular or plant organ proteomes [60-61], the characterization of genetic modifications [62-63], as well as others.

NaCl salinity [53]. Once again, a more integrated view is needed and deserves attention. These two studies commented above indicate the importance of mycorrhizal fungi regu‐ lation as a general strategy to protect plants from stress. If soil type is added to this equation, a much more complex situation is created and such an integrated study re‐ flects the reality of many agronomic situations. This also raises the question over the use of hydroponic systems to study oxidative stress in plants, particularly when induced by non-essential elements, since it is not necessarily the real field condition. Yet, is not our intention to say that such studies under hydroponic conditions are not important. On the contrary, they also have advantages. However, a more dynamic or integrated type of

A Comprehensive Survey of International Soybean Research - Genetics, Physiology, Agronomy and Nitrogen

Curiously, grafting, which is a well-known agronomic technique largely used in agriculture, has not been used much in studies of stress in plants. The grafting technique has a tremen‐ dous potential to add further important understanding about stress signaling, assimilation, transport and accumulation of metals, opening a new perspective to study these grafted plants at the biochemical and molecular levels. Unfortunately, very few examples are availa‐ ble in the literature focusing on the investigation of plant stress responses. An example of such a study is the one carried out by [54] who showed that Cd seed concentration can be influenced by the difference in translocation of Cd from soil to the seed and in Cd accumula‐

Nowadays, the development of plant manipulation techniques, for example the production and use of transgenic plants, has contributed to studies involving plant antioxidant respons‐ es induced either by exogenous or endogenous factors (such as herbicide, metals, pollution). Studies involving the mechanisms leading to stress-tolerant plants are important and need‐ ed, since they can aid understanding and create new possibilities for the use of these kinds of plants. The knowledge provided by the "omics studies" such as proteomics, metabolo‐ mics, metallomics and genomics, added to enzymatic evaluation, can provide information that can decisively help in answering many questions related to oxidative stress and ROS

Taking into account the importance of "omics" platforms, as well as their use for corroborat‐ ing our initial hypothesis, the following sections will focus on these important strategies. They will be divided into proteomics and metallomics, with brief descriptions of each one, as well as some discussions and examples regarding transgenic cultures, but always concen‐

Proteomics can be defined as the large-scale study of proteins, including not only their iden‐ tifications and quantifications, but also the determination of their localizations, modifica‐ tions, interactions, activities, and functions [55]. This information is extremely important to evaluate interactions between different proteins, or between proteins and other molecules, and may reveal the functional role of proteins [56]. In this sense, proteomics is an important

study should be considered in our point of view.

control [32].

Relationships

590

**3. Proteomics**

trating the focus on soybean.

tion capacity of roots among soybean cultivars by the use of grafting.

The insertion of exogen DNA fragments into the DNA of the target organism, to confer some enhanced characteristics to the latter, describes the process termed genetic modifica‐ tion [64]. Focusing on plants, improved productiveness, enhanced tolerance to herbicides, synthesis of new substances and others can have consequences related to genetic modifica‐ tion [64]. The natural responses to this process are known to change the protein map of an organism [65]. In this sense, comparative proteomics become the strategy of choice, being useful for establishing qualitative and quantitative differences between genetically and nongenetically modified organisms [66]. In this way, studies of protein changes are frequently carried out through polyacrylamide gels by evaluation of their images, providing relevant information for comparative proteomic studies [67,68] as well as using appropriate mass spectrometric techniques for evaluating the identity of the studied proteins [69-70].

For proteomic studies, gel electrophoresis separations are the most used platform, due to their high resolution, allowing either high efficiency protein separation or the identification of potential protein spots with differences in concentration or expression in the gels evaluat‐ ed [67,68]. The gel electrophoresis technique can be applied in proteomic studies as follow: (1) one-dimensional gel electrophoresis (SDS-PAGE) [71], (2) two-dimensional gel electro‐ phoresis (2-D PAGE) followed by manual image analysis [66] and (3) two-dimensional dif‐ ference gel electrophoresis (2-D DIGE) followed by automatic image analysis [72]. The application of these techniques in comparative studies involving transgenic soybeans has been little explored, where variation of different proteomic profiles in soybean genotypes [73], abiotic environmental stress [74], osmotic stress [75] and improvement of protein quali‐ ty in transgenic soybean plants [76] are examples found. In this way, the use of these separa‐ tion techniques in combination with mass spectrometry were applied in our research group to comparative proteomic studies in transgenic and non-transgenic soybean seeds, and it will be discussed below.
