Update on Plant Ionomics Update on Plant Ionomics

Living systems are supported and sustained by the genome through the action of the transcriptome, proteome, metabolome, and ionome, the four basic biochemical pillars of functional genomics. These pillars represent the sum of all the expressed genes, proteins, metabolites, and elements within an organism. The dynamic response and interaction of these biochemical ‘‘omes’’ defines how a living system functions, and its study, systems biology, is now one of the biggest challenges in the life sciences. Studies on the functional connections between the genome and the transcriptome (Martzivanou and Hampp, 2003; Becher et al., 2004; Leonhardt et al., 2004), proteome (Koller et al., 2002), and metabolome (Fiehn et al., 2000) are well under way; however, the study of the ionome, in contrast, is still in its infancy (Lahner et al., 2003; for review, see Hirschi, 2003; Rea, 2003), with the majority of genes and gene networks involved in its regulation still unknown. Moreover, because the ionome is involved in such a broad range of important biological phenomena, including electrophysiology, signaling, enzymology, osmoregulation, and transport, its study promises to yield new and significant biological insight. An understanding of the ionome and how it interacts with other cellular systems such as the genome, proteome, metabolome, and environment are integral to our full understanding of how plants integrate their organic and inorganic metabolisms. Lahner and colleagues first described the ionome to include all the metals, metalloids, and nonmetals present in an organism (Lahner et al., 2003), extending the term metallome (Outten and O’Halloran, 2001; Williams, 2001; Szpunar, 2004) to include biologically significant nonmetals such as nitrogen, phosphorus, sulfur, selenium, chlorine, and iodine. It is important to note here that the boundaries between the ionome, metabolome, and proteome are blurred. Compounds containing the nonmetals phosphorus, sulfur, or nitrogen, for example, would fall within both the ionome and metabolome, and metals such as zinc, copper, manganese, and iron in metalloproteins would fall within the proteome, or metalloproteome as it has been described (Szpunar, 2004). The elements to be measured in the ionome will be determined by their biological importance or environmental relevance, in conjunction with their amenability to quantitation. However, each element measured must be present in sufficient concentrations in the plant tissue so as to be well above the Limit of Quantitation, defined as the concentration equal to the signal from a blank plus 10 SDs of the blank signal.