Genetic engineering approaches have contributed significantly to understand the regulation of amino acid metabolism in plants. Such approaches can be expected to become major tools in future research on plant amino acid metabolism. So far, detailed studies on amino acid metabolism, using genetic engineering approaches, were limited to a narrow range of pathways, particularly the pathway of AAAM, the aspartate family pathway, and to some extent the pathways of proline and tryptophan metabolism (Kishor et al., 1995; Li and Last, 1996; Nanjo et al., 1999; Tozawa et al., 2001; Zhang et al., 2001). Similar approaches for dissecting metabolic pathways of other amino acids are needed.
Many of the studies discussed here have focused on biosynthetic pathways, while less effort has been devoted to amino acid catabolic pathways. As in the emerging progress of lysine catabolism (Galili et al., 2001), amino acid catabolic pathways may be important metabolic components in plant development, reproduction, and responses to stress. Therefore, in future research, more efforts should be devoted to the dissection of amino acid catabolic pathways.
Amino acid metabolism is strongly regulated by various metabolites, many of which are non-amino acids, which serve not only as signaling molecules but also as intermediate metabolites in metabolic pathways of amino acids sugars and lipids. One example of such metabolites is pyruvate that serves as a precursor for a number of amino acid carbohydrate and lipid molecules. In microorganisms, the regulatory or rate-limiting roles of such intermediate metabolites can be studied by feeding experiments. The multicellular and multiorgan nature of higher plants does not enable proper feeding experiments in all tissues of intact plants and therefore provides additional levels of complexity that render the dissection of metabolic fluxes much more difficult to predict and study than in microorganisms. Understanding the regulation of metabolic fluxes and the importance of rate-limiting metabolites in different plant organs cannot be easily done by feeding experiments alone. Hence, such studies will depend strongly on tissue-specific and/or condition-specific genetic engineering as well as on isotope-labeling studies.
The identification of regulatory networks of amino acid metabolism as well as possible complexes of enzymes that may regulate these networks is also needed. Such studies can be strongly assisted by genetic engineering approaches. For example, identification of enzyme and complexes can be obtained by expressing chimeric genes encoding epitope-tagged enzymes in transgenic plants. It is expected that interdisciplinary approaches, such as that of the ‘‘matrix effect’’ will contribute to unraveling interacting molecular, metabolic, and environmental signals that regulate the networks of amino acid metabolism.
Understanding the compound regulation of metabolic networks (amino acid metabolism is included as a part of these metabolic networks) can be aided by detailed analysis of a large number of metabolites as well as by detailed analysis of the spatial, temporal and developmental patterns of expression of genes encoding enzymes and regulatory proteins associated with these networks. Thus, modern approaches such as metabolic profiling, gene expression profiling in microarrays, and proteomics will be progressively used in these studies. These issues have not been discussed in this chapter due to space limitation. Yet, several recent publications (Hunter et al., 2002; Lee et al., 2002; Ruuska et al., 2002) illustrate how microarray analyses of gene expression in Arabidopsis and maize seeds uncovered specific spatial and temporal expression patterns of genes associated with the metabolism of sugars, lipids, amino acids, and storage proteins during seed development.
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