Coordinations between gene modules control the operation of plant amino acid metabolic networks

Using our "Gene Coordination" approach, we have identified in Arabidopsis plants two oppositely regulated groups of "highly coordinated" genes within the branched Asp-family network of Arabidopsis plants, which metabolizes the amino acids Lys, Met, Thr, Ile and Gly, as well as a single group of "highly coordinated" genes within the branched aromatic amino acid metabolic network, which metabolizes the amino acids Trp, Phe and Tyr. These genes possess highly coordinated adjustable negative and positive expression responses to various stress cues, which apparently regulate adjustable metabolic shifts between competing branches of these networks. We also provide evidence implying that these highly coordinated genes are central to impose intra- and inter-network interactions between the Asp-family and aromatic amino acid metabolic networks as well as differential system interactions with other growth promoting and stress-associated genome-wide genes.Our novel Gene Coordination elucidates that branched amino acid metabolic networks in plants are regulated by specific groups of highly coordinated genes that possess adjustable intra-network, inter-network and genome-wide transcriptional interactions. We also hypothesize that such transcriptional interactions enable regulatory metabolic adjustments needed for adaptation to the stresses.Being stationary organisms that are unable to move, plants represent a unique biological system that is highly adaptive to environmental stresses. The adaptation mechanisms of plants to stresses also involve coordinated adjustments of a large array of metabolic networks. Among those are metabolic networks containing amino acids as intermediate metabolites, which can either be incorporated into proteins, accumulate to high levels in response to specific cues, such as proline accumulation in response to salt stress [1], or serve as precursors for a large array of metabolites with multiple functions. Some of the metabolic networks of amino acids